/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#include "utils/psmnistmspreader.h"

using namespace std;
using namespace bol;

#define STRINGIFY(x) XSTRINGIFY(x)
#define XSTRINGIFY(x) #x

int main(int argc, char **argv){
  string mspfile((argc>1)?argv[1]:STRINGIFY(DATADIR) "/a.msp");

  ModificationDictionary dico;
  dico.put(new Modification("Cys_CAM C 57.052"));
  dico.put(new Modification("CAM_core K 43.02504"));
  dico.put(new Modification("Oxidation_HW HW 15.999"));
  dico.put(new Modification("Oxidation_M M 15.999"));
  
  PeptideModifier peptmodifier;
  peptmodifier.setModifdico(&dico);
  peptmodifier.addModif(dico["Cys_CAM"], true);
  peptmodifier.addModif(dico["CAM_core"], true);
  peptmodifier.addModif(dico["Oxidation_HW"], true);
  peptmodifier.addModif(dico["Oxidation_M"], true);

  PSMNistMSPReader reader;
  reader.setPeptideModifier(&peptmodifier);
  reader.open(mspfile);
  while(PeptideSpectrumMatch *pmatch=reader.nextMatch()){
    peptmodifier.printPeptide(cout, pmatch->peptide());
    cout<<endl;
    cout<<(*pmatch->spectrum())<<endl;
  }
}
